Downregulation of hsa-miR-132 and hsa-miR-129: non-coding RNA molecular signatures of Alzheimer’s disease

Alzheimer’s disease (AD) affects the elderly population by causing memory impairments, cognitive and behavioral abnormalities. Currently, no curative treatments exist, emphasizing the need to explore therapeutic options that modify the progression of the disease. MicroRNAs (miRNAs), as non-coding RNAs, demonstrate multifaceted targeting potential and are known to be dysregulated in AD pathology. This mini review focuses on two promising miRNAs, hsa-miR-132 and hsa-miR-129, which consistently exhibit differential regulation in AD. By employing computational predictions and referencing published RNA sequencing dataset, we elucidate the intricate miRNA-mRNA target relationships associated with hsa-miR-132 and hsa-miR-129. Our review consistently identifies the downregulation of hsa-miR-132 and hsa-miR-129 in AD brains as a non-coding RNA molecular signature across studies conducted over the past 15 years in AD research.


Introduction
Alzheimer's disease (AD) is the leading cause of dementia, presenting a significant socioeconomic burden within aging societies.AD is a progressive disorder that manifests at the molecular level long before clinically observable dementia symptoms emerge (Aisen et al., 2017;Knopman et al., 2021).It commences with a preclinical phase, characterized by the absence of symptoms, followed by mild cognitive impairment (MCI), progressing through mild, moderate, and severe late AD stages (Aisen et al., 2017;Jack et al., 2018).In over 95 percent of the cases, AD develops later in life (above 65 years) and does not directly result from genetic inheritance (Andrieu et al., 2015).Neuropathologically, AD is identified by the presence of extracellular amyloid plaques primarily composed of amyloid beta (Aβ) peptides and intracellular neurofibrillary tangles (NFTs) consisting of hyperphosphorylated tau (p-tau) in the hippocampus and cortex (Glenner and Wong, 1984;Brion et al., 1991;Buée et al., 2000;Congdon and Sigurdsson, 2018;Panza et al., 2019).The complex nature of 10.3389/fnmol.2024.1423340 the disease has posed challenges in pinpointing its exact cause, leading to a lack of curative treatments.Consequently, there is an urgent need to explore neuroprotective strategies that can modify the disease progression during its early stages.Noncoding RNAs are known for their regulatory roles in fine tuning the transcription and translation processes (Szafranski et al., 2015;Idda et al., 2018).MicroRNAs (miRNAs) are a subclass of short RNA molecules that regulate gene expression following transcription.On average they have 22 nucleotides, and they are expressed ubiquitously.They bind to specific regions of target genes [primarily at the 3 untranslated region (UTR), though not limited to it], resulting in reduced expression of target genes through degradation of mRNA or inhibition of translation (Bartel, 2018;Nagaraj et al., 2021).Emerging evidence suggests that miRNAs undergo dysregulation in the brain, cerebrospinal fluid (CSF), and blood of individuals with AD (Nagaraj et al., 2019;Takousis et al., 2019;Yoon et al., 2022).
Consistent downregulation of hsa-miR-132 and hsa-miR-129 in Alzheimer's disease brain Several miRNAs are dysregulated in the brains of AD patients across various brain regions compared to non-demented controls (Nagaraj et al., 2019;Takousis et al., 2019).Most promising miRNAs dysregulated in AD brains and their predictions to bind mRNA targets involved in tau pathology are shown in Figure 1A.Of note, only few of these predictions are experimentally validated and demands further deciphering.Interestingly, recent studies validated hsa-miR-132 and hsa-miR-129 as standout miRNAs in terms of downregulation in AD patients (Patrick et al., 2017;Wingo et al., 2022).In this mini review article, we focus primarily on two miRNAs (hsa-miR-132 and hsa-miR-129) and discuss about their constant downregulation across different brain regions in AD, according to diverse cohorts (Figures 1B-E).We shed lights on their location, expression level and miRNA-mRNA target relationship in the post-mortem brains.
There is consensus about the downregulation of hsa-miR-132 in AD across several studies (Figure 1D).Those focusing on the hippocampus, an early affected region, have yielded valuable insights into the differential expression level of miRNAs in this brain region.Cogswell et al. (2008) conducted qPCR experiments, revealing downregulation of hsa-miR-132 in the hippocampus, the frontal cortex and the cerebellum.Similarly, several studies have investigated miRNA expression with different methodologies in both hippocampal and cortical regions of the brain.For instance, Lau et al. (2013) employed nCounter, qPCR, and RNA sequencing techniques, detecting downregulation of hsa-miR-132 not only in the hippocampus but also in the prefrontal cortex and the temporal cortex.Likewise, Smith et al. (2015) performed qPCR and observed downregulation of hsa-miR-132 in the hippocampus, the frontal cortex, and the temporal cortex.Also, Annese et al. (2018) used qPCR and RNA sequencing, revealing downregulation of hsa-miR-132-5p and hsa-miR-132-3p not only in the hippocampus but also in the temporal gyrus and the frontal gyrus.In a different cohort, Hadar et al. (2018) performed qPCR experiments and found downregulation of hsa-miR-132 in the hippocampus.
Due to limitation in post-mortem hippocampal tissue availability, most of the studies focused solely on the cortex to identify the change in expression of miRNAs along the course of disease development.For example, Hébert et al. (2013) used qPCR and RNA sequencing, identifying downregulation of hsa-miR-132-5p in the temporal cortex.Wong et al. (2013) also found downregulation of hsa-miR-132 using qPCR in the temporal cortex.Pichler et al. ( 2017) utilized microarray and qPCR, detecting downregulation of hsa-miR-132 in the frontal cortex and temporal cortex.Additionally, Patrick et al. ( 2017) employed nCounter and found downregulation of hsa-miR-132 in the prefrontal cortex.Li and Cai (2021) used RNA sequencing, detecting downregulation of hsa-miR-132-5p and hsa-miR-132-3p in the inferior frontal gyrus and superior temporal gyrus (Li and Cai, 2021).Similarly, Dobricic et al. (2022b) used qPCR and RNA sequencing to identify the downregulation of hsa-miR-132-5p in the superior temporal gyrus and entorhinal cortex.In addition to hippocampus and cortex, other regions have been explored.For instance, Zhu et al. (2016) conducted in situ hybridization (ISH) experiments, identifying downregulation of hsa-miR-132 in the Nucleus basalis of Meynert.In a separate study by Hadar et al. (2018) using qPCR demonstrated significant downregulation of hsa-miR-132 in the olfactory bulb.

Conclusion
Overall, these studies consistently demonstrate, through different methodologies, the downregulation of hsa-miR-132 and hsa-miR-129 in various regions of the AD brain, including the hippocampus, the cortex, and the olfactory bulb.While the downregulation of hsa-miR-132-3p and hsa-miR-129-5p is notably observed in AD, similar downregulation patterns are also identified in the brains of other neurodegenerative conditions, including Parkinson's disease (Dobricic et al., 2022a).The regulatory effects of these miRNAs in both pathologies are yet to be fully understood.Furthermore, our observations indicate that only a few of the predicted targets exhibit an inverse relationship with the corresponding miRNA, while most of them remain unchanged.This intricate miRNA-mRNA interactions require further investigation to comprehend the mechanisms underlying AD.Additionally, factors such as the RNA integrity number (RIN) value may introduce bias into the findings.Moreover, a comprehensive understanding of proteomics data is highly necessary to properly identify the relevant core hub for these hsa-miR-132 and hsa-miR-129 targets in AD.Furthermore, most of the literature identifying dysregulated miRNAs in human AD post-mortem samples has used bulk sequencing techniques (Lau et al., 2013;Patrick et al., 2017;Dobricic et al., 2022a).This type of sequencing does not provide information about cell-typespecific miRNAs and their mRNA target expressions.To advance our knowledge in this area, single-cell sequencing is necessary in human AD post-mortem samples.Moreover, a recent singlecell sequencing study in the mice hippocampus, although not in an AD-relevant model, suggested that mmu-miR-132 regulates cell-type-specific microglial homeostasis (Walgrave et al., 2023).
Collectively, these findings significantly enhance our understanding of the dysregulation of specific miRNAs in Alzheimer's disease.Further investigation into cell-specific miRNA-mRNA target relationships and the associated regulatory pathways, as well as exploring the utility of miRNA expression changes as biomarkers throughout the disease's progression, may pave the way for potential therapeutic interventions.
FIGURE 1 miRNA-mRNA target predictions and expression of hsa-miR-132 and hsa-miR-129 in post-mortem AD brain tissue.(A) On Y-axis of the heatmap, most promising dysregulated miRNAs in AD brain are shown (Patrick et al., 2017; Nagaraj et al., 2019; Takousis et al., 2019) and on X-axis of the heatmap, mRNA targets involved in direct and associated pathways in tau pathology.Blue gradient is used to visualize the prediction strengths based on TargetScan context score.Darker blue indicates the stronger predictions (most negative TargetScan context score) and light blue indicates the weaker predictions (least negative TargetScan context score) (B,C) Chromosomal location of hsa-miR-132 (B) and hsa-miR-129 (hsa-miR-129-1 and hsa-miR-129-2) (C) with the subsequent process to obtain mature miRNAs.(D,E) hsa-miR-132 (D) and hsa-miR-129 (E) differential expression level in various brain regions across AD studies.Green for downregulation in AD brains compared to control brains.Study characteristics show the cohort comparisons and techniques used in respective studies."miR-" indicated in the figure refer to "hsa-miR."